Plant pathogen damage, whether in the crop field or flower garden, has been an expensive and nearly insurmountable problem since agriculture first began. Co-evolution of plant and pathogen defines two solutions: outwitting the pathogen or helping the plant. Our modern approach has been to do both, while simultaneously assuring that associated ecosystems are not permanently damaged.
Various approaches address the ongoing power struggle between plant and plant pathogen. Since many important pathogens fall into the category of “biotrophic” or healthy tissue-needing pathogens, most research is directed at understanding them. Another class of pathogens, the “necrotrophs,” flourish when plants are weakened. The present invention arises out of study of a necrotrophic relationship between pathogen and plant.
Even though plants do not have immune systems in the mammalian sense of specialized secretory cells, they do possess the ability to avoid or minimize pathogen-induced damage and/or disease. Prior to the present invention, it was thought that the most frequent route for a species to avoid “extinction by pathogens” was one of two ways: programmed cell death at a pathogen's invasion site, and random mutation during meiosis to alter the specificity of pathogen recognition.
Programmed cell death (or “apoptosis”) at the site of invasion is a well-characterized phenomenon in plants, with particular gene groups, especially the “NBS-LRR” (nucleotide binding site, leucine-rich repeat), being known as a rich source of resistance genes. In plant genomes that have been studied for the presence of NBS-LRR regions (approximately 45), all have been found to contain them. The present invention provides a previously-uncharacterized resistance gene from sorghum. 
The second type of extinction avoidance, crossover events and point mutations during meiosis, results in plants that have new disease resistance gene specificities. Any new trait makes it possible that any given environment can select that trait as preferred. Much research goes into accelerating this normal process via plant breeding programs and molecular biology. Designing and/or selecting preferred traits in plants is a worldwide, billion dollar industry, with consumer and/or legislative pressures favoring plant breeding over programs that result in “GMO” programs. The present invention provides wholesome methods to speed traditional plant breeding processes.
On the other side of the equation, pathogen physiology and genetics research are sources of knowledge that can lead to new herbicides, insecticides and fungicides. In a twist on the common approach, some agriculturists study the use of pathogens (primarily insects and fungi) to kill weeds. Fungal isolates have been disclosed in the past which selectively kill invasive species.
Target specificity to specific plant species is a desired attribute of any herbicide; however, herbicides that are overly specific have markets that are too small to justify investment. Tools that decrease the cost of bringing a very specific herbicide to market would benefit investors as well as the environment. The present invention provides methods to identify such environmentally-friendly and economically-feasible herbicides.
As an example to the tenets previously described, Sorghum bicolor is a dietary staple of more than 500 million people worldwide. In the United States, sorghum provides an economical alternative to corn for use as ethanol biomass. Moreover, sorghum does not produce gluten, making it particularly useful as an alternative to wheat in the making of food and a beverages for gluten-intolerant individuals.
Sorghum, like other grain crops, is a target for a variety of pathogens. Some sorghum pathogens enter the plant un-recognized, and impair the plant. Some individual sorghum plants, however, recognize biotrophic pathogens (via distinctive surface or secreted chemicals), and mount a successful hypersensitive response, causing the site of infection to wither and die. The localized cell death starves the biotrophic, prevents further damage, and saves the plant. In this way, successful individual plants live to breed and pass their life-saving trait to future generations. However, the same is true of individual pathogens; some avoid being recognized by these newly-sensitive plants. This recognition/non-recognition process is an “arms race” between pathogen and plant. Dramatic shifts in plant and pathogen populations appear within as little as ten years.
Milo disease of sorghum is an example of a plant disease caused by a necrotroph. A plant with Periconia infection has dark red discoloration on the roots and crown. The leaves become chlorotic and eventually die. The infected plants produce little or no grain.
However, some individual sorghum plants do not respond to Periconia. These non-reactive plants grow normally, even if exposed to the Periconia fungus. In other words, these non-reactive sorghum plants are resistant to milo disease by not responding to Periconia's chemical cues.
Susceptibility to Periconia peritoxin and milo disease is provided by a single, semi-dominant gene, Pc. Pc naturally mutates to the resistant pc allele at a rate of about one per 8000 gametes. This high level of instability is unidirectional: pc to Pc mutations have not been observed.
Understanding the phenomena of milo disease susceptibility and resistance in sorghum adds value to agricultural research, development and commercialization in a wide variety of plants, and for the benefit of a wide variety of consumers.
Moreover, the evolutionary battle of pathogen vs. plant will unfold indefinitely because plants and pathogens each have their own mechanisms for avoiding extinction. Therefore, any new means for: 1. accelerating new plant development; 2. accelerating new herbicide development; and/or 3. accelerating our common wisdom in any of these fields, is useful and needed. The present invention provides tools and methods related to all three of these goals.